Quantifying the extent to which existing reserves meet conservation objectives and identifying gaps in coverage are vital to developing systematic protected-area networks. Despite widespread recognition of the Philippines as a global priority for marine conservation, limited work has been undertaken to evaluate the conservation effectiveness of existing marine protected areas (MPAs). Targets for MPA coverage in the Philippines have been specified in the 1998 Fisheries Code legislation, which calls for 15% of coastal municipal waters (within 15 km of the coastline) to be protected within no-take MPAs, and the Philippine Marine Sanctuary Strategy (2004), which aims to protect 10% of coral reef area in no-take MPAs by 2020. We used a newly compiled database of nearly 1000 MPAs to measure progress toward these targets. We evaluated conservation effectiveness of MPAs in two ways. First, we determined the degree to which marine bioregions and conservation priority areas are represented within existing MPAs. Second, we assessed the size and spacing patterns of reserves in terms of best-practice recommendations. We found that the current extent and distribution of MPAs does not adequately represent biodiversity. At present just 0.5% of municipal waters and 2.7-3.4% of coral reef area in the Philippines are protected in no-take MPAs. Moreover, 85% of no-take area is in just two sites; 90% of MPAs are <1 km(2). Nevertheless, distances between existing MPAs should ensure larval connectivity between them, providing opportunities to develop regional-scale MPA networks. Despite the considerable success of community-based approaches to MPA implementation in the Philippines, this strategy will not be sufficient to meet conservation targets, even under a best-case scenario for future MPA establishment. We recommend that implementation of community-based MPAs be supplemented by designation of additional large no-take areas specifically located to address conservation targets.